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Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

ABSTRACT: Transcription was assessed in the human H522 NSCLC cell line after reexpression of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by adenovirus infection, after treatment with 5 micromolar 5-deAzacytidine or after treatment with 100nM Trichostatin A. Control treatments included infection with adenovirus expressing GFP and treatment with DMSO4 (vehicle control). The goal of the experiment was to identify target genes of the SWI/SNF complex and compart them to changes induced by DNA methylation and histone acetylation modifiers. One biological replicate of each treatment; 4 technical replicates of each treatment.

ORGANISM(S): Homo sapiens

SUBMITTER: Walter Vonn

PROVIDER: S-ECPF-GEOD-54033 | biostudies-other |

REPOSITORIES: biostudies-other

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Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

Project description:Transcription was assessed in the human H522 NSCLC cell line after reexpression of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by adenovirus infection, after treatment with 5 micromolar 5-deAzacytidine or after treatment with 100nM Trichostatin A. Control treatments included infection with adenovirus expressing GFP and treatment with DMSO4 (vehicle control). The goal of the experiment was to identify target genes of the SWI/SNF complex and compart them to changes induced by DNA methylation and histone acetylation modifiers.

2014-01-13 | GSE54033 | GEO

Comparison of BRG1 reexpression, TSA treatment and 5dAzaC treatment on gene expression in human NCI-H522 NSCLC cells

2014-01-13 | E-GEOD-54033 | biostudies-arrayexpress

Comparison of gene expression in control and BRG1-knockdown H358 cell lines

Project description:Transcription was assessed in the human H358 NSCLC cell line after knockdown of BRG1, one of the mutually exclusive subunits of the SWI/SNF chromatin remodeling complex, by 2 different shRNAs. One biolgical replicate of each treatment; 4 technical replicates of each treatment.

| S-ECPF-GEOD-58542 | biostudies-other

Effect of pioglitazone treatment on gene expression in NCI-H2347 lung cancer cells: time course experiment

Project description:Microarray studies was performed to analyze gene expression changes in NCI-H2347 cells after treatment with 50 µM pioglitazone for 12hr, 24hr and 48hrs. RNA samples, containing 3 replicates for each sample, were extracted from NCI-H2347 cells after treatment with pioglitazone or vhicle (DMSO) for 12hr, 24hr and 48hrs. After biotin labeling, samples were hybridized on the Illumina Human HT12v4.0 Expression Beadchip.

| S-ECPF-GEOD-59735 | biostudies-other

BRG1-mediated chromatin remodeling regulates differentiation and gene expression of T helper cells.

Project description:During T helper cell differentiation, distinct programs of gene expression play a key role in defining the immune response to an environmental challenge. How chromatin remodeling events at the associated cytokine loci control differentiation is not known. We found that the ATP-dependent remodeling enzyme subunit BRG1 was required for T helper 2 (Th2) differentiation and Th2 cytokine transcription. BRG1 binding to cytokine genes was regulated by the extent of differentiation, the extent of activation, and cell fate. BRG1 was required for some features of the chromatin structure in target genes (DNase I hypersensitivity and histone acetylation), suggesting that BRG1 remodeling activity was directly responsible for changes in gene expression. NFAT and STAT6 activity were required for BRG1 recruitment to the Th2 locus control region, and STAT6 associated with BRG1 in a differentiation-inducible manner, suggesting direct recruitment of BRG1 to the bound loci. Together, these findings suggest BRG1 interprets differentiation signals and plays a causal role in gene regulation, chromatin structure, and cell fate.

| S-EPMC2593447 | biostudies-literature

YAP regulates PD-L1 expression in human NSCLC cells.

Project description:Programmed death-ligand 1 (PD-L1) is a membrane protein on tumor cells that binds to the PD-1 receptor expressed on immune cells, leading to the immune escape of tumor cells. Yes-associated protein (YAP) is a main effector of the Hippo/YAP signaling pathway, which plays important roles in cancer development. Here we show that YAP regulates PD-L1 expression in human non-small cell lung cancer (NSCLC) cells. First, we investigated YAP and PD-L1 expression at the protein level in 142 NSCLC samples and 15 normal lung samples. In tumor tissue, immunohistochemistry showed positive staining for YAP and PD-L1, which correlated significantly (n = 142, r = 0.514, P < 0.001). Second, in cell lines that express high levels of PD-L1 (H460, SKLU-1, and H1299), the ratio of p-YAP/YAP was lower and GTIIC reporter activity of the Hippo pathway was higher than those in three cell lines expressing low levels of PD-L1 (A549, H2030, and PC9) (P < 0.05). Third, in the same three cell lines, inhibition of YAP by two small interfering RNAs (siRNAs) decreased the mRNA and protein level of PD-L1 (P < 0.05). Fourth, forced overexpression of the YAP gene rescued the PD-L1 mRNA and protein level after siRNA knockdown targeting 3'UTR of the endogenous YAP gene. Finally, chromatin immunoprecipitation (ChIP) assays using a YAP-specific monoclonal antibody resulted in the precipitation of PD-L1 enhancer region encompassing two putative TEAD binding sites. Our results indicate that YAP regulates the transcription of PD-L1 in NSCLC.

| S-EPMC5777715 | biostudies-literature

Differential gene expression by NKX2-1 suppression in NCI-H2009 cells

Project description:The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To better understand how genomic alterations of NKX2-1 drive tumorigenesis, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma, and analyzed DNA binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation from NKX2-1-amplified human lung adenocarcinoma cell lines. Combining these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1, in addition to consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif in NKX2-1-bound sequences. RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1; cistromic analysis that NKX2-1 may cooperate with FOXA1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transducer of lineage specific cell survival of NKX2-1-amplified lung adenocarcinomas. NCI-H2009 cells with stable expression of either pLKO-Tet-Op-shGFP (n=4) or pLKO-Tet-Op-shNKX2-1 (pooled population; n=3 and a clone; n=3) were treated with 50ng/ml of doxycyline for 48 hours. Total RNA was extracted, gene expression profiling was performed and differential gene expression between shGFP and shNKX2-1 was analyzed to determine the effects by suppression of NKX2-1 in NCI-H2009 cells.

| S-ECPF-GEOD-40270 | biostudies-other

Comparison of Gene Expression in Human Embryonic Stem Cells, hESC-Derived Mesenchymal Stem Cells and Human Mesenchymal Stem Cells.

Project description:We present a strategy to identify developmental/differentiation and plasma membrane marker genes of the most primitive human Mesenchymal Stem Cells (hMSCs). Using sensitive and quantitative TaqMan Low Density Arrays (TLDA) methodology, we compared the expression of 381 genes in human Embryonic Stem Cells (hESCs), hESC-derived MSCs (hES-MSCs), and hMSCs. Analysis of differentiation genes indicated that hES-MSCs express the sarcomeric muscle lineage in addition to the classical mesenchymal lineages, suggesting they are more primitive than hMSCs. Transcript analysis of membrane antigens suggests that IL1R1(low), BMPR1B(low), FLT4(low), LRRC32(low), and CD34 may be good candidates for the detection and isolation of the most primitive hMSCs. The expression in hMSCs of cytokine genes, such as IL6, IL8, or FLT3LG, without expression of the corresponding receptor, suggests a role for these cytokines in the paracrine control of stem cell niches. Our database may be shared with other laboratories in order to explore the considerable clinical potential of hES-MSCs, which appear to represent an intermediate developmental stage between hESCs and hMSCs.

| S-EPMC3166576 | biostudies-literature

Regulation of PTEN expression by the SWI/SNF chromatin-remodelling protein BRG1 in human colorectal carcinoma cells.

Project description:BackgroundAberrant expression of Brahma-related gene-1 (BRG1), a core component of the SWI/SNF chromatin-remodelling complex, has been implicated in cancer development; however, the biological significance of BRG1 in colorectal carcinoma (CRC) remains unknown.MethodsIn CRC tissues, expression of BRG1 and Brahma (BRM) was investigated immunohistochemically. Colorectal carcinoma-derived DLD-1 cells were used for knockdown of BRG1 and PTEN with small interfering RNA (siRNA) and transduction of Akt. Complementary DNA (cDNA) microarray analysis was performed to explore the genes affected by BRG1.ResultsExpression of BRG1, but not BRM, was frequently elevated in CRC specimens, and knockdown of BRG1 suppressed cell proliferation of DLD-1 cells. By cDNA microarray, we determined that PTEN expression was negatively regulated by BRG1 in DLD-1 cells, which subsequently influenced the cyclin D1 levels via the phosphoinositide 3-OH kinase (PI3K)-Akt signalling pathway. The interplay of BRG1 on cyclin D1 expression was confirmed by the introduction of Akt and knockdown of PTEN in the BRG1 siRNA-transduced DLD-1 cells. Interestingly, this positive correlation between BRG1 and cyclin D1 expression was also observed in CRC specimens.ConclusionBrahma-related gene-1 has an important role in the process of CRC development by activating the PI3K-Akt signalling pathway and resultant upregulation of cyclin D1 levels.

| S-EPMC3039810 | biostudies-literature

Human lung cancer cell lines DMS-273 (SCLC) and NCI-H1437 (NSCLC): scrambled vs. shRNA clones

Project description:Transcriptional profiling of two human lung cancer cell lines, DMS-273 (small cell lung cancer) and NCI-H1437 (non-small cell lung cancer), stably transfected either with innocuous scrambled shRNAs or SETDB1-specific.The objective was to identify global gene expression changes due to the depletion of the H3K9me3 methyltransferase SETDB1. 3 replicates for DMS-273 and 1 Control; 2 replicates for NCI-H1437 and 1 Control

| S-ECPF-GEOD-45175 | biostudies-other

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